Is CEBPA p.Pro23= (c.69G>A) pathogenic?

CEBPA p.Pro23= (c.69G>A) is classified Likely benign in CEBPA (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-03). Very rare (popmax 0.00154%, afr); Associated with Inborn genetic diseases.

What condition is associated with CEBPA p.Pro23= (c.69G>A)?

CEBPA p.Pro23= (c.69G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CEBPA p.Pro23= (c.69G>A) in the general population?

CEBPA p.Pro23= (c.69G>A) is very rare (popmax 0.00154%, afr) (gnomAD).

CEBPA p.Pro23=

c.69G>A · VCV4827148

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00154%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.074	GERP -2.3, phastCons 0.73
Overall
CADD	9.145	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00154% African / African-American · 1/64,960 alleles

Overall 7.43e-05% 1/1,346,584 alleles · very rare exomes 1/1,195,074 · genomes 0/151,510 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CEBPA
Protein: p.Pro23=
Coding: c.69G>A
MANE Select: NM_004364
Type: single nucleotide variant
Location: chr19:33302346 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 23: the 'required to repress e2f1:tfdp1-mediated transcription, to inhibit cell cycle and to induce adipocyte differentiation' region; the 'disordered' region

Full CEBPA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEBPA p.Pro23Arg Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro23Ser Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro23Gln Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro23Thr Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro23Leu Uncertain significance ★ ⚠ same residue
CEBPA c.-1C>A Uncertain significance ★★ same condition
CEBPA c.-4C>G Uncertain significance ★★ same condition
CEBPA p.Ala118Thr Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cebpa-p-pro23 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown